Structure

Physi-Chem Properties

Molecular Weight:  363.34
Volume:  422.0
LogP:  6.377
LogD:  3.968
LogS:  -5.624
# Rotatable Bonds:  17
TPSA:  16.35
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.203
Synthetic Accessibility Score:  2.678
Fsp3:  0.783
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.002
MDCK Permeability:  1.3056064744887408e-05
Pgp-inhibitor:  0.009
Pgp-substrate:  1.0
Human Intestinal Absorption (HIA):  0.791
20% Bioavailability (F20%):  0.859
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.458
Plasma Protein Binding (PPB):  74.61908721923828%
Volume Distribution (VD):  1.061
Pgp-substrate:  33.5402717590332%

ADMET: Metabolism

CYP1A2-inhibitor:  0.064
CYP1A2-substrate:  0.935
CYP2C19-inhibitor:  0.113
CYP2C19-substrate:  0.905
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.062
CYP2D6-inhibitor:  0.983
CYP2D6-substrate:  0.574
CYP3A4-inhibitor:  0.018
CYP3A4-substrate:  0.253

ADMET: Excretion

Clearance (CL):  7.695
Half-life (T1/2):  0.234

ADMET: Toxicity

hERG Blockers:  0.189
Human Hepatotoxicity (H-HT):  0.25
Drug-inuced Liver Injury (DILI):  0.041
AMES Toxicity:  0.009
Rat Oral Acute Toxicity:  0.776
Maximum Recommended Daily Dose:  0.038
Skin Sensitization:  0.939
Carcinogencity:  0.092
Eye Corrosion:  0.978
Eye Irritation:  0.925
Respiratory Toxicity:  0.982

Download Data

Data Type Select
General Info & Identifiers & Properties  
Structure MOL file  
Source Organisms  
Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC235589

Natural Product ID:  NPC235589
Common Name*:   QVLQCDBLHFENOC-UHFFFAOYSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  QVLQCDBLHFENOC-UHFFFAOYSA-N
Standard InCHI:  InChI=1S/C12H6S/c1-3-5-7-11-9-10-12(13-11)8-6-4-2/h1,4,9-10H,2H2
SMILES:  C#CC#Cc1ccc(C#CC=C)s1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   5315560
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000097] Thiophenes
        • [CHEMONTID:0003481] 2,5-disubstituted thiophenes

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO21382 Eutypa lata Species Diatrypaceae Eukaryota n.a. n.a. n.a. PMID[12608846]
NPO2842 Garcinia lucida Species Clusiaceae Eukaryota n.a. n.a. n.a. PMID[17880175]
NPO3925 Bursera microphylla Species Burseraceae Eukaryota Resin Baha de Kino 2013-JAN PMID[25966052]
NPO3925 Bursera microphylla Species Burseraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO3925 Bursera microphylla Species Burseraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO20648 Streptomyces cellulosae Species Streptomycetaceae Bacteria n.a. n.a. n.a. Database[UNPD]
NPO20718 Hypericum elegans Species Hypericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21507 Ephedra intermedia Species Ephedraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19837 Euonymus latifolius Species Celastraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20431 Centaurea canariensis Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20101 Eria acutifolia Species Orchidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19410 Clutia abyssinica Species Peraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17908 Rhododendron reticulatum Species Ericaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3925 Bursera microphylla Species Burseraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17115 Kielmeyera petiolaris Species Calophyllaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO26309 Ahnfeltiopsis flabelliformis Species Phyllophoraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2842 Garcinia lucida Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19559 Cetraria pseudocomplicata Species Parmeliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20295 Eclipta prostrata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14172 Rhopaloeides odorabile Species Spongiidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18749 Corydalis vernyi Species Papaveraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO11034 Mnium pseudopunctatum Species Mniaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20233 Marchantia paleacea Species Marchantiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21251 Tabernaemontana odoratissima Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO20982 Morus lactea Species Sulidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21382 Eutypa lata Species Diatrypaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19272 Alcyonium fauri Species Alcyoniidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3468 Astragalus floccosifolius Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  NP Quantity Composition/Concentration

Organism ID NP ID Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

  Biological Activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

  Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

●  The left chart: Distribution of similarity level between NPC235589 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID

  Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC235589 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage

  Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data